4h04
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==Lacto-N-biosidase from Bifidobacterium bifidum== | |
| + | <StructureSection load='4h04' size='340' side='right'caption='[[4h04]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[4h04]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_bifidum_JCM_1254 Bifidobacterium bifidum JCM 1254]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H04 FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4h04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h04 OCA], [https://pdbe.org/4h04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h04 RCSB], [https://www.ebi.ac.uk/pdbsum/4h04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h04 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/LNBB_BIFB1 LNBB_BIFB1] Present in the infant gut, this enzyme is involved in the assimilation of type-1 human milk oligosaccharides (HMOs). It hydrolyzes via a retaining mechanism the beta-D-GlcNAc-(1->3)-beta-D-Gal linkage in lacto-N-tetraose (LNT or beta-D-Gal-(1->3)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-D-Glc), an abundant HMO unique to human breast milk, releasing lacto-N-biose (LNB or beta-D-Gal-(1->3)-D-GlcNAc) and lactose (PubMed:18469123, PubMed:23479733). Is a key enzymatic factor for growth and proliferation of B.bifidum in the gut ecosystem of breast-fed infants (Probable). Has substrate preference for unmodified beta-linked LNB since it does not hydrolyze the fucosylated forms of lacto-N-tetraose (lacto-N-fucopentaose I and II) or lacto-N-neotetraose. Is also able to display transglycosylation activity in vitro (PubMed:18469123).<ref>PMID:18469123</ref> <ref>PMID:23479733</ref> <ref>PMID:23479733</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Human milk oligosaccharides contain a large variety of oligosaccharides, of which lacto-N-biose I (Gal-beta1,3-GlcNAc; LNB) predominates as a major core structure. A unique metabolic pathway specific for LNB has recently been identified in the human commensal bifidobacteria. Several strains of infant gut-associated bifidobacteria possess lacto-N-biosidase, a membrane-anchored extracellular enzyme, that liberates LNB from the nonreducing end of human milk oligosaccharides and plays a key role in the metabolic pathway of these compounds. Lacto-N-biosidase belongs to the glycoside hydrolase family 20, and its reaction proceeds via a substrate-assisted catalytic mechanism. Several crystal structures of GH20 beta-N-acetylhexosaminidases, which release monosaccharide GlcNAc from its substrate, have been determined, but to date, a structure of lacto-N-biosidase is unknown. Here, we have determined the first three-dimensional structures of lacto-N-biosidase from Bifidobacterium bifidum JCM1254 in complex with LNB and LNB-thiazoline (Gal-beta1,3-GlcNAc-thiazoline) at 1.8-A resolution. Lacto-N-biosidase consists of three domains, and the C-terminal domain has a unique beta-trefoil-like fold. Compared with other beta-N-acetylhexosaminidases, lacto-N-biosidase has a wide substrate-binding pocket with a -2 subsite specific for beta-1,3-linked Gal, and the residues responsible for Gal recognition were identified. The bound ligands are recognized by extensive hydrogen bonds at all of their hydroxyls consistent with the enzyme's strict substrate specificity for the LNB moiety. The GlcNAc sugar ring of LNB is in a distorted conformation near (4)E, whereas that of LNB-thiazoline is in a (4)C1 conformation. A possible conformational pathway for the lacto-N-biosidase reaction is discussed. | ||
| - | + | Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum.,Ito T, Katayama T, Hattie M, Sakurama H, Wada J, Suzuki R, Ashida H, Wakagi T, Yamamoto K, Stubbs KA, Fushinobu S J Biol Chem. 2013 Apr 26;288(17):11795-806. doi: 10.1074/jbc.M112.420109. Epub, 2013 Mar 11. PMID:23479733<ref>PMID:23479733</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 4h04" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Bifidobacterium bifidum JCM 1254]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Ashida H]] | ||
| + | [[Category: Fushinobu S]] | ||
| + | [[Category: Ito T]] | ||
| + | [[Category: Katayama T]] | ||
| + | [[Category: Suzuki R]] | ||
| + | [[Category: Wada J]] | ||
| + | [[Category: Wakagi T]] | ||
| + | [[Category: Yamamoto K]] | ||
Current revision
Lacto-N-biosidase from Bifidobacterium bifidum
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